GLYA_BRADU
ID GLYA_BRADU Reviewed; 432 AA.
AC P24060;
DT 01-MAR-1992, integrated into UniProtKB/Swiss-Prot.
DT 28-FEB-2003, sequence version 2.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Serine hydroxymethyltransferase {ECO:0000255|HAMAP-Rule:MF_00051};
DE Short=SHMT {ECO:0000255|HAMAP-Rule:MF_00051};
DE Short=Serine methylase {ECO:0000255|HAMAP-Rule:MF_00051};
DE EC=2.1.2.1 {ECO:0000255|HAMAP-Rule:MF_00051};
GN Name=glyA {ECO:0000255|HAMAP-Rule:MF_00051}; OrderedLocusNames=bll5033;
OS Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 /
OS NBRC 14792 / USDA 110).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Bradyrhizobiaceae; Bradyrhizobium.
OX NCBI_TaxID=224911;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=USDA 110spc4;
RX PubMed=2014004; DOI=10.1111/j.1365-2958.1991.tb01824.x;
RA Rossbach S., Hennecke H.;
RT "Identification of glyA as a symbiotically essential gene in Bradyrhizobium
RT japonicum.";
RL Mol. Microbiol. 5:39-47(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110;
RX PubMed=12597275; DOI=10.1093/dnares/9.6.189;
RA Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S.,
RA Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M.,
RA Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S.;
RT "Complete genomic sequence of nitrogen-fixing symbiotic bacterium
RT Bradyrhizobium japonicum USDA110.";
RL DNA Res. 9:189-197(2002).
CC -!- FUNCTION: Catalyzes the reversible interconversion of serine and
CC glycine with tetrahydrofolate (THF) serving as the one-carbon carrier.
CC This reaction serves as the major source of one-carbon groups required
CC for the biosynthesis of purines, thymidylate, methionine, and other
CC important biomolecules. Also exhibits THF-independent aldolase activity
CC toward beta-hydroxyamino acids, producing glycine and aldehydes, via a
CC retro-aldol mechanism. {ECO:0000255|HAMAP-Rule:MF_00051}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O =
CC (6S)-5,6,7,8-tetrahydrofolate + L-serine; Xref=Rhea:RHEA:15481,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15636, ChEBI:CHEBI:33384,
CC ChEBI:CHEBI:57305, ChEBI:CHEBI:57453; EC=2.1.2.1;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00051};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00051};
CC -!- PATHWAY: One-carbon metabolism; tetrahydrofolate interconversion.
CC {ECO:0000255|HAMAP-Rule:MF_00051}.
CC -!- PATHWAY: Amino-acid biosynthesis; glycine biosynthesis; glycine from L-
CC serine: step 1/1. {ECO:0000255|HAMAP-Rule:MF_00051}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00051}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00051}.
CC -!- SIMILARITY: Belongs to the SHMT family. {ECO:0000255|HAMAP-
CC Rule:MF_00051}.
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DR EMBL; X54638; CAA38450.1; -; Genomic_DNA.
DR EMBL; BA000040; BAC50298.1; -; Genomic_DNA.
DR PIR; S15203; S15203.
DR RefSeq; NP_771673.1; NC_004463.1.
DR RefSeq; WP_011087794.1; NZ_CP011360.1.
DR AlphaFoldDB; P24060; -.
DR SMR; P24060; -.
DR STRING; 224911.27353298; -.
DR EnsemblBacteria; BAC50298; BAC50298; BAC50298.
DR GeneID; 64024795; -.
DR KEGG; bja:bll5033; -.
DR PATRIC; fig|224911.44.peg.4897; -.
DR eggNOG; COG0112; Bacteria.
DR HOGENOM; CLU_022477_2_1_5; -.
DR InParanoid; P24060; -.
DR OMA; SHPAGLI; -.
DR PhylomeDB; P24060; -.
DR UniPathway; UPA00193; -.
DR UniPathway; UPA00288; UER01023.
DR Proteomes; UP000002526; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0004372; F:glycine hydroxymethyltransferase activity; IBA:GO_Central.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IBA:GO_Central.
DR GO; GO:0070905; F:serine binding; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IBA:GO_Central.
DR GO; GO:0046655; P:folic acid metabolic process; IBA:GO_Central.
DR GO; GO:0019264; P:glycine biosynthetic process from serine; IBA:GO_Central.
DR GO; GO:0006565; P:L-serine catabolic process; IBA:GO_Central.
DR GO; GO:0006730; P:one-carbon metabolic process; IBA:GO_Central.
DR GO; GO:0035999; P:tetrahydrofolate interconversion; IEA:UniProtKB-UniPathway.
DR GO; GO:0046653; P:tetrahydrofolate metabolic process; IBA:GO_Central.
DR CDD; cd00378; SHMT; 1.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR HAMAP; MF_00051; SHMT; 1.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR InterPro; IPR001085; Ser_HO-MeTrfase.
DR InterPro; IPR019798; Ser_HO-MeTrfase_PLP_BS.
DR InterPro; IPR039429; SHMT-like_dom.
DR PANTHER; PTHR11680; PTHR11680; 1.
DR Pfam; PF00464; SHMT; 1.
DR PIRSF; PIRSF000412; SHMT; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR PROSITE; PS00096; SHMT; 1.
PE 3: Inferred from homology;
KW Amino-acid biosynthesis; Cytoplasm; One-carbon metabolism;
KW Pyridoxal phosphate; Reference proteome; Transferase.
FT CHAIN 1..432
FT /note="Serine hydroxymethyltransferase"
FT /id="PRO_0000113544"
FT BINDING 131
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT BINDING 135..137
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT SITE 239
FT /note="Plays an important role in substrate specificity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT MOD_RES 240
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT CONFLICT 73
FT /note="R -> L (in Ref. 1; CAA38450)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 432 AA; 46035 MW; 2D3F6EA0F0D2A235 CRC64;
MTSAKTASAP DSFFTASLDQ ADPEIAAAIK GELGRQRHEV ELIASENIVS RAVLEAQGSV
MTNKYAEGYP GARYYGGCEW VDVAENLAID RAKKLFGAGF ANVQPNSGSQ MNQAVFLALL
QPGDTFMGLD LAAGGHLTHG SPVNMSGKWF KAAHYTVRRE DQIIDMDAVQ KQAEEIKPKL
IVAGGSAYSR AWDFKRFREI ADSVGAYLLV DMAHFAGLVA GGVHASPVPY AHVTTTTTHK
SLRGPRGGLI LSNDETLAKK LNSAIFPGLQ GGPLMHVIAA KAVAFGEALR PDFKVYAKNV
VENAKALAEA MKSHGFDIVS GGTDNHLMLV DLRPKGLKGN VSEKALVRAA ITCNKNGIPF
DPEKPFVTSG LRLGTPAATT RGFGVAEFQQ VGGMIAEVLN AIAQSDDGKA PLVEAAIKER
VKALTDRFPI YQ
